Push for Better Death Data Bears Fruit: Largest Ever Global Dataset of Individual Deaths Released

Jocalyn Clark @jocalynclark comments on the INDEPTH Network’s release of the largest ever dataset of individual deaths in Africa and Southeast Asia, and the importance of equality in health data.

Enthusiasts of global health research will have observed various battles over the years about ‘the best’ health data and estimates. On one side are sophisticated mathematical models arising from advanced statistical techniques but often patchy data, including the massive Global Burden of Disease (GBD) studies.

On another side are on-the-ground collections of individual deaths, using techniques such as verbal autopsy where data collectors actually interview the family members of the deceased and determine cause of death. In 2010 PLOS Medicine devoted a Collection (which I commissioned) to the global health estimates debate, much of which seems highly relevant four years later.

Both types of health information generate insights into the patterns and magnitude of different diseases around the world. And in truth these ‘sides’ should not be pitted against each other – as their estimates and data complement each other. For death data in particular, there appear to be shared aims to generate better quality and more accurate information about what people die from, not least because it helps us determine which interventions and investments are needed to prevent those deaths. Nevertheless, how and by whom global mortality estimates are generated can often inspire anxiety and antagonism.

Continue reading »

Category: General | 3 Comments

Does Exposure to Smoking (Either Passive or Active) Lead to Increased Allergies?

Charles Ebikeme interviews Dr. Bahi Takkouche of the University of Santiago de Compostela and reviews his research on smoking and allergies, which was published earlier this year in PLOS Medicine.

Dr. Takkouche’s paper is included in the PLOS Clinical Immunology Collection, which is organized into broad categories in response to the commonly articulated request from our users that we provide more structured and efficient access to papers of interest in the PLOS corpus. The Collection has been updated today with two new sections on Immunodeficiency and Autoimmune Diseases.

Smoking is one of the most common factors when you think of allergens. Its link to a whole host of diseases within the atopic march – the cascade of allergies that starts with allergic dermatitis (such as eczema) during infancy, progresses to allergic rhinitis (for example hay fever) and food allergies, and finally exhibits with asthma – has been heavily researched. But unfortunately, no clear consensus exists as to the causes.

Research published in PLOS Medicine in March of 2014 took a wide look at the data from all published research on the theme of tobacco smoking and its relation to allergies. The sheer volume of amassed and analysed knowledge often makes it difficult for good recommendations to be made to practitioners on the risks involved with – let alone other researchers in the field wanting to see where their work fits in the landscape. A meta-analysis like this allows all studies to be assessed together, and gives a clearer picture of the research landscape.
Continue reading »

Category: General | 6 Comments

An Interview with Pascale Cossart

Charles Ebikeme interviews Pascale Cossart of the Institut Pasteur on the occasion of her receipt of the Women in Science Award at FEBS-EMBO 2014.

Pascale CossartOn September 2, Pascale Cossart received the Women in Science Award at the Federation of European Biochemical Societies / EMBO 2014 conference.

On October 23, Cossart and colleagues published “Listeria monocytogenes Dampens the DNA Damage Response” in PLOS Pathogens, in which she describes a toxin that blocks the body’s response to bacterial induced DNA, a crucial step for a productive infection.


Why did you decide to become a scientist? What drew you to the field?

At the beginning I decided to become a scientist because I loved science. I was interested in chemistry. But after two weeks in a chemistry lab I realized that maybe I loved it on paper, but I had the feeling that the big period of chemistry was somehow over. I was in organic chemistry and polymer chemistry, then I took a course — par hasard — of biochemistry, and then I went to my professor and I switched–and that was it. But I never had any other aim than doing research. I remember that my parents were telling me that I could make more money in industry instead of having this little fellowship.

Continue reading »

Category: General | Tagged , , , | 1 Comment

Pneumonia Affects People of All Ages: Interview with Carlos J. Orihuela

For World Pneumonia Day 2014PLOS Pathogens interviews Associate Editor, author, and researcher Carlos J. Orihuela on his recent publication in PLOS Pathogens, Streptococcus pneumoniae Translocates into the Myocardium and Forms Unique Microlesions That Disrupt Cardiac Function, describing how the disease can lead to heart damage in the elderly.

High powered magnification of the 30 h cardiac microlesion shows S. pneumoniae bacterial aggregates within the microlesion.

High powered magnification of the 30 h cardiac microlesion shows S. pneumoniae bacterial aggregates within the microlesion.

Continue reading »

Category: General | Tagged , , , , | Comments Off on Pneumonia Affects People of All Ages: Interview with Carlos J. Orihuela

What Factors Might Have Led to the Emergence of Ebola in West Africa?

This manuscript has been conditionally accepted by PLOS Neglected Tropical Diseases for publication prior to formal review. Following a successful outcome of independent peer review, a revised version will be formally published by PLOS Neglected Tropical Diseases and a link to the final article posted here. Read more here

A PDF of the full text is available: Alexander et al.

What factors might have led to the emergence of Ebola in West Africa?

K.A. Alexander¹, C.E. Sanderson¹, M. Marathe2,3, B.L. Lewis³, C.M. Rivers³, J. Shaman4, J.M. Drake5, E. Lofgren³, V.M. Dato6, M.C. Eisenberg7, and S. Eubank³

1 Department of Fisheries and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia

2 Department of Computer Science, Virginia Tech, Blacksburg, Virginia.

3 Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia.

4 Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York

5 Odum School of Ecology, University of Georgia, Athens, Georgia

6 Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania

7 Departments of Epidemiology and Mathematics, University of Michigan, Ann Arbor, Michigan


An Ebola outbreak of unprecedented scope emerged in West Africa in December 2013 and presently continues unabated in the countries of Guinea, Sierra Leone, and Liberia. Ebola is not new to Africa and outbreaks have been confirmed as far back as 1976. The current West African Ebola outbreak is the largest ever recorded and differs dramatically from prior outbreaks in its duration, number of people affected, and geographic extent. The emergence of this deadly disease in West Africa invites many questions, foremost among these: Why now and why in West Africa? Here, we review the sociological, ecological, and environmental drivers that might have influenced the emergence of Ebola in this region of Africa and its spread throughout the region. Containment of the West African Ebola outbreak is the most pressing, immediate need. A comprehensive assessment of the drivers of Ebola emergence and sustained human-to-human transmission is also needed in order to prepare other countries for importation or emergence of this disease.  Such assessment includes identification of country-level protocols and interagency policies for outbreak detection and rapid response, increased understanding of cultural and traditional risk factors within and between nations, delivery of culturally embedded public health education, and regional coordination and collaboration, particularly with governments and health ministries throughout Africa. Public health education is also urgently needed in countries outside of Africa in order to ensure that risk is properly understood and public concerns do not escalate unnecessarily. To prevent future outbreaks, coordinated, multiscale, early warning systems should be developed that make full use of these integrated assessments, partner with local communities in high-risk areas, and provide clearly defined response recommendations specific to the needs of each community.

Competing Interests: The authors have declared that no competing interests exist.

Funding: The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.This work has been partially supported by DTRA CNIMS Contract HDTRA1-11-D-0016-0001. Research reported in this publication was partially supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number 5U01GM070694-11 and U01 GM110748 as well as the RAPIDD program of the Science and Technology Directorate, US Department of Homeland Security and the NLM Pittsburgh Biomedical Informatics Training Grant 5T15 LM007059-28.

Copyright: © 2014 Alexander et al. This is an open-access manuscript distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Continue reading »

Category: Ebola, General | 9 Comments

Mind the Deadly Gaps

Grania Brigden (@TBBrigden) discusses the urgent need to close the gaps in the TB response.

Image Credit: Treatment Action Group

Image Credit: Treatment Action Group

The 45th Union World Conference on Lung Health held in Barcelona last week opened with the Health Ministers of South Africa and India making bold statements and commitments to address and reverse the TB epidemics in their countries. Five other countries also committed to ending TB, resulting in the birth of the Barcelona Declaration on TB.

This political commitment is desperately needed. The recently published WHO Global TB Report 2014 highlighted not only the increasing numbers but also the growing crisis in tackling drug-resistant TB. The reality for those infected with multi-drug resistant TB (MDR-TB) is that they have only a one in eight chance of being identified, correctly diagnosed, started on treatment and cured. This is not acceptable.

Continue reading »

Category: General, MSF, Tuberculosis | Tagged | 2 Comments

EMA’s Release of Regulatory Data: Possible Fall out for Journals and Research Synthesis

On 2 October the European Medicines Agency’s (EMA) published the final version of its policy on prospective release of clinical study reports (CSRs) of trials submitted by sponsors in support of Marketing Authorisation Applications (MAAs).

I have summarized its content and made preliminary comments here

The policy

Image credit: gosheshe, Flickr

Image credit: gosheshe, Flickr

In brief, from 1 January 2015 the proactive policy will join the current reactive policy and allow prospective access to incomplete CSRs at two levels: a “viewer” level of access and a “researcher” level. The former will allow on-screen viewing only with a simple registration procedure, while the latter will require proof of identity but allow download and OCR searches to be carried out on CSRs. Prospective seems to mean two things: after a regulatory decision has been taken, pharma will format and write CSRs for direct web posting, and once you have obtained access credentials, you will not have to ask every time you want a CSR and wait some months (and in some cases be turned down).

Its meaning

The practical importance of the policy hinges on the dawning realization of the difference in accuracy, completeness and trustworthiness of published versions of trials compared to their CSR counterparts. Trials may not be published, some may not even be registered (especially the older ones) posing decades-old problems for readers, users and, from my point of view, evidence synthetisers. Reporting bias (cherry picking) is the broad term which encompasses the scores of different types of bias present in publications. The range from the well-known publication bias to the less known swamping bias (when important information on a trial is missed amidst a sea of other information). CSRs in theory cut through all this by presenting exhaustive structured narratives and results of trials. This is essentially part of what regulators see.

The policy has some as yet unclear legal aspects and sets out equally unclear rules for redaction of CSRs (based on the preservation of commercial interests and protection of participant privacy). It also does not explain why some parts of the CSRs will not be released.

Continue reading »

Category: General | 2 Comments

Social Pathways for Ebola Virus Disease in Rural Sierra Leone, and some Implications for Containment

The below manuscript was initially posted here on October 31st, 2014 following its conditional acceptance by PLOS Neglected Tropical Diseases for publication prior to formal review. The paper has achieved a successful outcome of independent peer review and the final version was formally published on April 17th, 2015. That version is available here

Social pathways for Ebola Virus Disease in rural Sierra Leone, and some implications for containment

Paul Richards¹*, Joseph Amara¹, Mariane C Ferme², Prince Kamara¹, Esther Mokuwa¹, Amara Idara Sheriff¹, Roland Suluku¹, and Maarten Voors³

1 Njala University, Sierra Leone

2 University of California, Berkeley, United States of America

3 Wageningen University, The Netherlands

*Corresponding author: paul.richards@wur.nl.


The current outbreak of Ebola Virus Disease in Upper West Africa is the largest ever recorded.  Molecular evidence suggests spread has been almost exclusively through human-to-human contact.  Social factors are thus clearly important to understand the epidemic and ways in which it might be stopped, but these factors have so far been little analyzed.  The present paper focuses on Sierra Leone, and provides data on the least understood part of the epidemic – the largely undocumented spread of Ebola in rural areas.  Various forms of social networking in rural communities and their relevance for understanding pathways of transmission are described.  Particular attention is paid to the relationship between marriage, funerals and land tenure.  Funerals are known to be a high-risk factor for infection.  It is suggested that more than a shift in awareness of risks will be needed to change local patterns of behavior, especially in regard to funerals, since these are central to the consolidation of community ties.  A concluding discussion relates the information presented to plans for halting the disease.  Local consultation and access are seen as major challenges to be addressed.

Competing Interests: The authors have declared that no competing interests exist.

Funding: International Initiative for Impact Evaluation (3ie) through the Global Development Network (GDN) grant #TW1.1042 to MV and PR, http://www.3ieimpact.org/en/  UK Economic and Social Research Council (ESRC) grant # ES/J017620/1 to MV and PR, http://www.esrc.ac.uk/ National Science Foundation, grant # 1430959 to MF, http://www.nsf.gov FAO and Irish Aid funds to EM and PR, http://www.fao.org/home/en/  https://www.irishaid.ie/The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Copyright: © 2014 Richards et al. This is an open-access manuscript distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Beyond zoonosis

The present outbreak of Ebola Virus Disease (EVD) in Upper West Africa is the worst ever recorded.  Currently (late September 2014) it has a case doubling rate of three weeks, and shows no signs of coming under control.  The international community is alarmed, and resources are being rushed to the region to try and stem further spread.  The epidemic is an outbreak of the Zaire strain of the virus, previously associated with death rates of up to 90 per cent.  Death rates in the Upper West African outbreak average 70 percent (WHO 2014)

The epidemic has been traced to a single index case – the infection of a 2 year-old boy in the village of Meliandou, in the Republic of Guinea (Baize et al 2014, Bausch and Schwarz 2014). Previous outbreaks of the disease have occurred in remote forest edge communities, and have been associated with hunting and eating of bush meat.  This scenario appears not to be appropriate for the present epidemic.  Human-to-human transmission appears to be the main if not sole source of infection.

In this paper we offer some data and observations relating to the Sierra Leone epidemic (Figure 1).  If human-to-human contact is the main mode of transmission attention needs to be paid to underlying social factors.  The paper is divided into three sections.  A case-study based scenario for the spread of EVD in Sierra Leone is described (based on interviews and direct observation by two Njala-based authors of the present paper, RS and JA), and proposes greater attention should be paid to rural buffers for the disease.  We then identify and explain the role of processes related to marriage, land and burials significant for spread of the disease.  A concluding discussion considers what assistance might be necessary if rural communities are to reduce current transmission rates.

Continue reading »

Category: Ebola, General | 10 Comments

A Rapid Response to Ebola

November 11th 2014 Update: Two manuscripts have now been posted to Speaking of Medicine and can be viewed here:

Social Pathways for Ebola Virus Disease in Rural Sierra Leone, and some Implications for Containment

What factors might have led to the emergence of Ebola in West Africa?

Original Post:

The ability to rapidly disseminate the findings of primary research as well as informed scientific assessment and opinion is critical in the face of public health emergencies such as the present outbreak of the Ebola virus.  At PLOS, primary research findings can be rapidly and effectively distributed through PLOS Currents: Outbreaks. The unmet need to provide expert commentary and insightful opinion on Ebola as rapidly has led PLOS Neglected Tropical Diseases to carefully select expert opinion, social science assessment, or topic reviews for public posting on Speaking of Medicine before formal and rigorous peer review.

The authors of manuscripts identified by the Editors as suitable are offered the opportunity to post their text with the understanding that, because of its quality and likely favorable review, is conditionally accepted for publication in the journal.  Authors are required to provide confirmation of authorship as well as financial disclosure and competing interest statements, which will be posted along with the text.

The Editors of PLOS Neglected Tropical Diseases are excited to provide a platform to make available much needed information publicly, openly, responsibly, and as quickly as possible.

For questions or further information, please contact PLOS NTDs Publications Manager Jeri Marie Wright at jwright@plos.org

Category: Ebola, General | 2 Comments

Researchers Follow the Path of HIV and Prevention Interventions

Charlene Dezzutti from the University of Pittsburgh and the Magee-Womens Research Institute explains how HIV researchers are incorporating biomarkers and preclinical testing – featured in the PLOS Collection Advances in HIV Mucosal Immunology: Challenges and Opportunities – in their pursuit of an effective HIV preventative such as a topical microbicide gel or an oral pill containing anti-retroviral drugs or a vaccine.

Biomarkers are biological substances that mark the presence of a disease or condition in a person. For instance, cholesterol level is a biomarker for heart disease and CD4+ T cell counts or plasma HIV RNA levels are biomarkers for HIV disease progression. Biomarkers are important because they allow physicians to track an individual patient’s condition during treatment to better predict and improve health outcomes.

Image Credit: Artistic rendition of immune cells and potential HIV targets in the rectal mucosal. Yang, Ochoa, Preza & Anton, 2014

Image Credit: Artistic rendition of immune cells and potential HIV targets in the rectal mucosal. Yang, Ochoa, Preza & Anton, 2014

Likewise, biomarkers of product safety and efficacy would provide a tremendous benefit to the HIV prevention field because they would help identify preventatives that are safe and effective. Since newly developed experimental products cannot be tested in humans, models that accurately predict how humans would react – called “preclinical models” – are used. Because HIV in adults is usually transmitted sexually, with the exception of intravenous drug users, researchers have been targeting the tissues and routes that first encounter the virus to better understand the dynamic host-pathogen interaction.  Researchers are now working to develop and test animal and ex vivo tissue culture models to try and predict how these new HIV prevention products will work in people. The latest models use human mucosal tissue and secretions as well as non-human primates to mimic as closely as possible human exposures and potential responses.
Continue reading »

Category: General | 1 Comment